I've no direct experience comparing these two, however, something to consider here is that, according to the designer of both components, TB (with comments having been passed along by PD), Fono MM is intended to be superior to the MM stages within any of the integrated amps. No specific details have been forthcoming, however, one can surmise via a combination of what has been published and what can be seen.
"The Fono MM MK5 uses a fully discrete, cascaded, complementary amplifier input stage, a configuration designed to optimise the performance of your moving magnet cartridge."
The above isn't meant to suggest that the whole stage is fully discrete, as, like those within the integrated amps, there is an op-amp present, only the input stage employs discrete circuitry. The same can be said about those within the integrated amps, only there is one major distinguishing factor that isn't mentioned, but which can easily be seen under the hood of Fono MM, specifically, a not just dedicated, but also regulated power supply. Fono takes 24VAC in via the supplied wall-wart adapter but then regulates this further via an internal supply that includes 2 x reservoir capacitors plus a voltage regulator circuit, the latter not unlike those used in Naim and Exposure power supplies, all located well away from the discrete input stage (considering the small space within).
Rega Fono VER#2 ISS3 PCB pictured below. Easier to identify components than with the later SMT board(s). Note RE63 looks like it says 'REG3'.